A benchmark-driven modelling approach for evaluating deployment choices on a multi-core architecture

The complexity of current and emerging architectures provides users with options about how best to use the available resources, but makes predicting performance challenging. In this work a benchmark-driven model is developed for a simple shallow water code on a Cray XE6 system, to explore how deployment choices such as domain decomposition and core affinity affect performance. The resource sharing present in modern multi-core architectures adds various levels of heterogeneity to the system. Shared resources often includes cache, memory, network controllers and in some cases floating point units (as in the AMD Bulldozer), which mean that the access time depends on the mapping of application tasks, and the core's location within the system. Heterogeneity further increases with the use of hardware-accelerators such as GPUs and the Intel Xeon Phi, where many specialist cores are attached to general-purpose cores. This trend for shared resources and non-uniform cores is expected to continue into the exascale era. The complexity of these systems means that various runtime scenarios are possible, and it has been found that under-populating nodes, altering the domain decomposition and non-standard task to core mappings can dramatically alter performance. To find this out, however, is often a process of trial and error. To better inform this process, a performance model was developed for a simple regular grid-based kernel code, shallow. The code comprises two distinct types of work, loop-based array updates and nearest-neighbour halo-exchanges. Separate performance models were developed for each part, both based on a similar methodology. Application specific benchmarks were run to measure performance for different problem sizes under different execution scenarios. These results were then fed into a performance model that derives resource usage for a given deployment scenario, with interpolation between results as necessary.

Balanced Ocean-Data Assimilation near the Equator

The question is addressed whether using unbalanced updates in ocean-data assimilation schemes for seasonal forecasting systems can result in a relatively poor simulation of zonal currents. An assimilation scheme, where temperature observations are used for updating only the density field, is compared to a scheme where updates of density field and zonal velocities are related by geostrophic balance. This is done for an equatorial linear shallow-water model. It is found that equatorial zonal velocities can be detoriated if velocity is not updated in the assimilation procedure. Adding balanced updates to the zonal velocity is shown to be a simple remedy for the shallow-water model. Next, optimal interpolation (OI) schemes with balanced updates of the zonal velocity are implemented in two ocean general circulation models. First tests indicate a beneficial impact on equatorial upper-ocean zonal currents.

Understanding the tsunami with a simple model

In this paper, we use the approximation of shallow water waves (Margaritondo G 2005 Eur. J. Phys. 26 401) to understand the behaviour of a tsunami in a variable depth. We deduce the shallow water wave equation and the continuity equation that must be satisfied when a wave encounters a discontinuity in the sea depth. A short explanation about how the tsunami hit the west coast of India is given based on the refraction phenomenon. Our procedure also includes a simple numerical calculation suitable for undergraduate students in physics and engineering.

Numerical Experimental Comparison of Dam Break Flows with non-Newtonian Fluids

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Envenomation by a benthic Hydrozoa (Cnidaria): the case of Nemalecium lighti (Haleciidae)

A case of envenomation caused by the Nemalecium lighti is described. The hydrozoan species lives in many kinds of substrates, being quite common in tropical shallow water. The patient, a marine biologist, had contact with the animal in two different opportunities while snorkeling. Both contacts produced erythematous and highly pruriginous papules in exposed areas of the body. The signs and symptoms persisted for a week and healed without sequellae. (C) 2001 Elsevier B.V. Ltd. All rights reserved.

Bite by moray eel

Injuries caused by moray eels are not a common problem, but are distributed throughout the globe, affecting mainly fishermen while manipulating hooked or netted fish. on a lesser scale, scuba divers and snorkelers, practicing or not spear fishing, are occasional victims of bites. With more than 185 species distributed among 15 genera, mostly in tropical to temperate shallow water, moray eels easily come into contact with humans and occasional injuries are not uncommon. The current study reports one case of moray eel bite and discusses the circumstances in which the accident happened, as well as wound evolution and therapy.

Caracterização de reservatórios siliciclásticos neoaptianos: um estudo do membro carmópolis no campo de Camorim, sub-bacia de Sergipe, Brasil

The Camorim Oilfield, discovered in 1970 in the shallow water domain of the Sergipe Sub-basin, produces hydrocarbons from the Carmópolis Member of the Muribeca Formation, the main reservoir interval, interpreted as siliciclastics deposited in an alluvial-fluvial-deltaic context during a late rifting phase of Neoaptian age, in the Sergipe-Alagoas Basin. The structural setting of the field defines different production blocks, being associated to the evolution of the Atalaia High during the rift stage and subsequent reactivations, encompassing NE-SW trending major normal faults and NWEW trending secondary faults. The complexity of this field is related to the strong facies variation due to the interaction between continental and coastal depositional environments, coupled with strata juxtaposition along fault blocks. This study aims to geologically characterize its reservoirs, to provide new insights to well drilling locations in order to increase the recovery factor of the field. Facies analysis based on drill cores and geophysical logs and the 3D interpretation of a seismic volume, provide a high resolution stratigraphic analysis approach to be applied in this geodynamic transitional context between the rift and drift evolutionary stages of the basin. The objective was to define spatial and time relations between production zones and the preferential directions of fluid flow, using isochore maps that represent the external geometry of the deposits and facies distribution maps to characterize the internal heterogeneities of these intervals, identified in a 4th order stratigraphic zoning. This work methodology, integrated in a 3D geological modelling process, will help to optimize well drilling and hydrocarbons production. This methodology may be applied in other reservoirs in tectonic and depositional contexts similar to the one observed at Camorim, for example, the oil fields in the Aracaju High, Sergipe Sub-basin, which together represent the largest volume of oil in place in onshore Brazilian basins

Spatial and seasonal distributions of Callinectes danae (Decapoda, Portunidae) in Ubatuba Bay, São Paulo, Brazil

The spatial and seasonal distributions of Callinectes danae Smith, 1869, in Ubatuba Bay, São Paulo, Brazil, were investigated as a part of a broad study on the general biology of portunids along the northern coast of São Paulo State, Brazil. Swimming crabs were collected during one year, from September 1995 to August 1996, along eight transects determined according to local physiographic features. Three replicate trawls were performed monthly at each transect. Depth. salinity, dissolved oxygen, temperature, organic matter content, and texture of the sediment were measured. Callinectes danae individuals were concentrated in shallow water close to the discharge of estuaries where the bottom is composed of fine and very fine sand. The species was more abundant in the warmer months. During the study period, C. danae exhibited continuous reproduction with a peak of reproductive intensity in June. Within this area, some sites are particularly favorable for C. danae establishment due to a combination of factors and prevailing local conditions.

Population biology of shrimp Macrobrachium jelskii (Miers, 1778) (Decapoda, Palaemonoidea) at the Grande River at northwest of the state of Minas Gerais, Brazil

OBJETIVO: A biologia populacional do camarão de água doce Macrobrachium jelskii foi investigada, com ênfase na distribuição de frequência em classes de tamanho, razão sexual, período reprodutivo e recrutamento juvenil. Além disso, a abundância dos indivíduos foi correlacionada com os fatores abióticos. MÉTODOS: Amostras foram coletadas mensalmente de julho de 2005 a junho de 2007, às margens do Rio Grande, região de Planura, estado de Minas Gerais, Brasil (20º 09' S e 48º 40' W), usando uma rede de arrasto (1.0 mm tamanho da malha e 2.0 × 0.5 m de largura). O equipamento foi arrastado por duas pessoas às margens da vegetação do rio por 100 metros de distância, percorridos por uma hora. em laboratório, os espécimes foram identificados, mensurados e sexados. RESULTADOS: Um total de 2,789 espécimes foi analisado, no qual correspondem a 1,126 machos (549 jovens e 577 adultos) e 1,663 fêmeas (1,093 jovens, 423 adultos não ovígeras e 147 ovígeras). A razão sexual diferiu significativamente a favor de fêmeas de M. jelskii (1:1.48; χ² = 103.95; p < 0.0001). A média de tamanho do comprimento da carapaça (CL) das fêmeas (6.32 ± 1.84 mm CL) foi estatisticamente maior do que dos machos (5.50 ± 1.07 mm CL) (p < 0.001). A distribuição de freqüência em classes de tamanho dos espécimes revela um padrão de distribuição unimodal e não normal para machos e fêmeas (W = 0.945; p < 0.01). Não foi observada relação entre a abundância de M. jelskii e as variáveis ambientais (p = 0.799). CONCLUSÃO: A presença de fêmeas ovígeras e jovens na população sugere um padrão de reprodução e recrutamento contínuos para M. jelskii na região de Planura.

SYSTEMATICS, TAPHONOMY, and PALEOECOLOGY of HOMALONOTID TRILOBITES (PHACOPIDA) FROM THE PONTA GROSSA FORMATION (DEVONIAN), PARANA BASIN, BRAZIL

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Composição e abundância da ictiofauna de duas lagunas costeiras da América do Sul Austral: lagoa do Peixe (31ºS; 51ºW), Brasil e laguna Mar Chiquita (37ºS; 57ºW), Argentina

This article describes and compares the shallow water fish-fauna from two coastal lagoons (Peixe Lagoon, in Brazil, and Mar Chiquita Lagoon, in Argentina). Peixe Lagoon was sampled between 2000 and 2001 using a 9 m beach seine net (12 mm bar mesh in the wings and 5 mm in the centre 3 m section) totalizing 125 samples, which yielded 33,848 individuals and 32 species. Mar Chiquita Lagoon was sampled from 1995 to 1998 using a 21) m beach seine net (12 mm bar mesh) totalizing 232 samples resulting in 31,097 individuals of 28 species. A total of 47 species were observed in both lagoons and 13 were shared. The "marine-estuarine-related" species were similar and dominate the fish assemblages in both lagoons. The remaining species were similar to the species collected along the southern Brazil, Uruguay and Argentina estuaries. The number of species observed in Peixe Lagoon (S = 32) was higher than in Mar Chiquita Lagoon (S = 28) and is probably associated with a strong latitudinal gradient of species richness increasing from north to south. Considering that the Peixe Lagoon and Mar Chiquita Lagoon are isolated by the large estuaries of Patos Lagoon and Prata River, the composition of the species with low abundance and occasional occurrence were different for each local studied. These results expand the knowledge for the fauna of both sites and help conservation and management from both lagoons.

Asymptotic soliton train solutions of Kaup-Boussinesq equations

Asymptotic soliton trains arising from a 'large and smooth' enough initial pulse are investigated by the use of the quasiclassical quantization method for the case of Kaup-Boussinesq shallow water equations. The parameter varying along the soliton train is determined by the Bohr-Sommerfeld quantization rule which generalizes the usual rule to the case of 'two potentials' h(0)(x) and u(0)(x) representing initial distributions of height and velocity, respectively. The influence of the initial velocity u(0)(x) on the asymptotic stage of the evolution is determined. Excellent agreement of numerical solutions of the Kaup-Boussinesq equations with predictions of the asymptotic theory is found. (C) 2003 Elsevier B.V. All rights reserved.

Recent brachiopods from the southern Brazilian shelf: Palaeontological and biogeographical implications

Until recently, the rhynchonelliform (articulated) brachiopod fauna from the Brazilian continental shelf (western South Atlantic) was represented only by the endemic species Bouchardia rosea (Mawe), reported from coastal waters of the states of São Paulo and Rio de Janeiro. The present study, based on samples from coastal (<30 m), shelf, and continental slope waters (99-485 m), documents the South Atlantic brachiopod fauna and shows that this fauna is more widespread, diverse, and cosmopolitan than previously thought. Based on a total of 16,177 specimens, the following brachiopods have been identified: Bouchardia rosea (Family Bouchardiidae), Platidia anomioides (Family Platidiidae), Argyrotheca cf. cuneata (Family Megathyrididae), and Terebratulina sp. (Family Cancellothyrididae). In coastal settings, the fauna is overwhelmingly dominated by Bouchardia rosea. Rare juvenile (<2 mm) specimens of Argyrotheca cf. cuneata were also found at two shallow-water sites. In shelf settings (100-200 m), the fauna is more diverse and includes Bouchardia rosea, Terebratulina sp., Argyrotheca cf. cuneata, and Platidia anomioides. Notably, Bouchardia rosea was found in waters as deep as 485 m, extending the known bathymetric range of this genus. Also, the record of this brachiopod in waters of the state of Parana is the southernmost known occurrence of this species. The genera Platidia and Terebratulina are documented here for the first time for the western South Atlantic. The Brazilian brachiopod fauna shares similarities with those from the Atlantic and Indian shelves of southern Africa, and from the Antarctic, Caribbean and Mediterranean waters. The present-day brachiopods of the western South Atlantic are much more cosmopolitan than previously thought and their Cenozoic palaeobiogeographic history has to be reconsidered from that perspective.

Changes in coral reef communities and an associated reef fish species, Cephalopholis cruentata (Lacepede), after 30 years on Curacao (Netherlands Antilles)

Using the same methodology and identical sites, we repeat a study dating from 1973 and quantify cover of hard coral species, soft corals, sponges, hard substratum and soft substratum, and density of a commercially important reef fish species, the graysby Cephalopholis cruentata, along a depth-gradient of 3-36 m oil the coral reefs of Curacao. The objective was to determine the multi-decade change in benthic coral reef cover and structural complexity, and their effect oil densities of an associated reef fish species. Total hard coral cover decreased on average from 52% in 1973 to 22% in 2003, representing a relative decline of 58%. During this time span, the cover of hard substratum increased considerably (from 11 to 58%), as did that of soft corals (from 0.1 to 2.2%), whereas the cover of sponges showed no significant change. Relative decline of hard coral cover and of reef complexity was greatest in shallow waters (near the coast), which is indicative of a combination of anthropogenic influences from shore and recent storm damage. Cover of main reef builder coral species (Agaricia spp., Siderastrea siderea, Montastrea annularis) decreased more than that of other species, and resulted in a significant decrease in reef complexity. Although density of C. cruentata was highly correlated to cover of Montastrea and Agaricia in 1973, the loss of coral cover did not show any effect on the total density of C. cruentata in 2003. However, C. cruentata showed a clear shift in density distribution from shallow water in 1973 to deep water in 2003. It call be concluded that the reefs of Curacao have degraded considerably in the last three decades, but that this has had no major effect on the population size of one commercially important coral-associated fish species.

Microfacies and sequence stratigraphy of the Amapa Formation, Late Paleocene to Early Eocene, Foz do Amazonas Basin, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)